So what's the problem? The cferror tag allows you to specify a file to run when an error occurs. The file is relative to the Application.cfm file. So if an error occurs in /foo/moo/goo.cfm, and your Application.cfm file in root simply says to load "error.cfm", which exists in root, then it wil load just fine.
However - if you take the exact same cferror tag and place it in an Application.cfc file - the template value is now considered relative to the page causing the error - not the Application.cfc file. You can get around this by using a mapping - but obviously it is something to look out for. You can also use an onError method as well, but if the onError does a cfinclude, you most likely need to use a mapping as well. Actually - let me test that. So a quick test shows that a cfinclude in onError will be relative to the Application.cfc file.